public Translation(Gene gene, Substance aa) {
if (gene != null) {
setGene(gene);
setName("Translation_" + gene.getName());
setSystem(gene.getGeneticSystem());
}
if (aa != null) {
setAminoAcid(aa);
}
setToPrint(false);
}
// print formatted info in no particular order
public String getInfoString() {
String s = "<HTML>";
// gene info
if (geneInfoSet) {
s += "<B>";
if (gene.getGeneType().equals(Gene.geneType.ENTREZ)) {
s += "Entrez Gene";
} else if (gene.getGeneType().equals(Gene.geneType.ENSEMBL)) {
s += "Ensembl Gene";
}
s += "</B><BR>";
String name = gene.getName();
if (name != null) s += "Name: " + name + "<BR>";
String description = gene.getDescription();
if (description != null) s += "Description: " + description + "<BR>";
String chromosome = gene.getChromosome();
if (chromosome != null) s += "Chromosome: " + chromosome + "<BR>";
s += "Start: " + gene.getStart() + "<BR>";
s += "End: " + gene.getEnd() + "<BR>";
s += "<BR>";
}
Iterator it = attributes.keySet().iterator();
while (it.hasNext()) {
String node = (String) it.next();
if (node.equals("Graphics")) continue;
s += "<B>" + node + "</B><BR>";
Iterator currentIt = attributes.get(node).keySet().iterator();
while (currentIt.hasNext()) {
String key = (String) currentIt.next();
s += key + ": " + attributes.get(node).get(key) + "<BR>";
}
s += "<BR>";
}
s += "</HTML>";
return s;
}
public boolean equals(Object o) {
if (!(o instanceof Gene)) return false;
Gene gene = (Gene) o;
return gene.getName().compareTo(name) == 0;
}
@Override
public int compareTo(Gene gene) {
return gene.getName().compareTo(name);
}
@Override
protected Void doInBackground() throws Exception {
int count = 0;
String sep = "\t";
try {
PrintWriter writer = new PrintWriter(file);
writer.write("Feature_Number" + sep);
writer.write("Location" + sep);
writer.write("Gene_name" + sep);
writer.write("Gene_accession" + sep);
writer.write("Gene_Location" + sep);
writer.write("distance_to_tss" + "\n");
for (Region r : feature.getRegions()) {
Peak peak = (Peak) r;
String chrom = peak.chrom;
if (geneData.hasKey(chrom)) {
int index = geneData.getNCList(chrom).getOverlapIndex(peak);
Vector<Region> preGenes = new Vector<Region>();
Vector<Region> nearGenes;
Vector<Region> postGenes = new Vector<Region>();
if (index > 0) {
preGenes = geneData.getNCList(chrom).getRegionsAt(index - 1);
}
nearGenes = geneData.getNCList(chrom).getRegionsAt(index);
if (index + 1 < geneData.getNCList(chrom).size()) {
postGenes = geneData.getNCList(chrom).getRegionsAt(index + 1);
}
nearGenes.addAll(preGenes);
nearGenes.addAll(postGenes);
Gene nearestGene = null;
long min_dist = Long.MAX_VALUE;
for (Region testPeak : nearGenes) {
// print(testPeak.getClass().toString());
Gene g = (Gene) testPeak;
long dist = getDistToTss(peak, g);
if (dist < min_dist) {
min_dist = dist;
nearestGene = (Gene) testPeak;
}
} // end for, each close gene.
writer.write(count + sep);
writer.write(peak.getLocationString() + sep);
writer.write(nearestGene.getName() + sep);
writer.write(nearestGene.getAccession() + sep);
writer.write(nearestGene.getLocationString() + sep);
writer.write(min_dist + "\n");
} // end if, has same chromosome key
++count;
} // end for, each peak region
writer.close();
} catch (Exception ex) {
ex.printStackTrace();
}
return null;
}
